City of Storms and Bones
by Ayame Isana
Summary: Jocelyn fearing the worst sent her son to another dimension, Elemental Nation. Now 5 years old Naruto gains his sight and sees the downworlder's learning demonology from warlocks, survival training from werewolves, plants and herbs from faeries and just having fun with vampires, soon Naruto becomes a Shadowhunter ninja. Pairing: Jace x Clary, Alec x Magnus
1. Rebirth

**Ayame: This is my very first fanfiction EVER! *squeal***

**Ayame: Ok, so not everything you read is grammar perfect so bear with me ;)**

**DISCLAIMER: AYAME DOES NOT OWN MORTAL INSTRUMENT OR NARUTO *sobs in her emo corner***

_**Now let's start!**_

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_There is nothing sadder than a child who has barely seen the world, yet who has seen enough of it to know that he does not wish to be a part of it...  
_  
**City of Storms and Bones**  
_**Prologue**_

A woman with beautiful red hair ran through the forest, behind her was the sound of battle, swords clashing, sounds of metal tearing through flesh and cries of fear and anguish.

"Mama, where we going?"

A healthy boy with the most beautiful azure eyes, a perfect sun-kissed tan and a mop of blonde hair.

"Shhh, Jonathan, please be quiet." She told her son which her son obeyed. A tall figure of a teen with bluish hair, golden cat like eyes and was dressed for battle met her view.

"Your late Jocelyn." He said waiting for the woman to catch her breath, "Is that the child?" Pointing at the child who has staring at him with curiosity.

"Yes, his name is Jonathan" She smiled lovingly at her son who smiled back, she then stared at the man seriously, "but enough about him, tell me can you do it?"

"Maybe, maybe not, look lady this isn-" He was slammed into a tree a stele a the nip of his neck. He fearfully looked at her face, he froze as angry emerald eyes seem to see right_ through_ him.

"Can you or can you not?! I don't have time, Magnus!" She cried angrily at the warlock sending killer intent at him, he froze unable to stand at such killer intent. Usually Magnus was stronger then this, hell he could stand in front of a Demon Lord and not even flinch but this... the wrath of a mother was _very_ frightening.

"Y-yes, but I-I'm not sure i-if I-I can send him t-to a pacific l-location." Magnus stuttered in fear. Jocelyn began to tremble at the thought, she glanced at her baby who was hiding behind.

"But will he be away from here?" She asked quietly, Magnus nodded his head in response. Jocelyn clenched her chest in despair. "Alright."

"Jonathan" She cooed at the boy, "my baby, be a strong boy ok, drink lots of milk, take baths and go to sleep early too, study h-hard and a-alway remember I-I love y-you!" Jocelyn cried hugging the baby in her arms.

"Are you alright? Should I start the spell now?" Magnus asked a crying mother, Jocelyn took deep breaths and gave a small nod.

"Yes Magnus, start the spell."

The next time Jonathan opened his eyes he was being cradled in the arms of a woman who looked like his mother. She was speaking to him but he couldn't understand her, but if Jonathan had to guess, _"Ashiteru Naruto!"_ Probably meant I love you or something like that.

He was then grabbed by a man, Jonathan cried as he was pulled away from his mother figure. Jonathan took a look at the man, he was blond and had azure blue eyes, his skin was tanned perfectly and he a perfect build, not to bulky but not to skinny either.

_'Is he my father?'_ Jonathan thought looking at the older man. He began to compare himself from his father.  
They both had blonde hair and that blue eyes that Mama always loved.

Jonathan then stopped crying, his hand quivered a little as he grabbed his father's coat. The blond grabbed the boy and disappeared in a yellow flash. He appeared in a battle field where a giant demonic fox with nine tails tore through the village destroying anything in it's path.

Jonathan shivered in fear, burying his face in the his father's trench coat. He got dizzy as his father began to run in a incredible burst of speed but the last thing Jonathan remembered was some sort of seal being drawn on his stomach and immense pain.

**TBC**

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**Ayame: So what d'ya think? **  
**Ayame: Please tell me what you think and review!**  
**Ayame: Jonathan is five years old before he was reborn into Naruto and was already well trained by his parents.**


	2. The Weird Blue Haired Guy

**Chapter 1: The Weird Blue Haired Guy**  
**Naruto/Jonathan's POV**  
Let me introduce myself to you. My name is Naruto Uzumaki. I'm five years old and I'm currently learning to be a ninja. I live by myself in the slums of the village Konoha. Not I mind, actually it's pretty cool there _especially_ neighborhood parties.

Anyway, lately I've been noticing some stuff, _creepy_ stuff. There was this one time, when an old lady across the street looked like she was going to eat me, _literally!_ And I swear I saw her hand turn into a bones, it was like that ninja thing, you know genjutsu. Then this other time when I was in the forest, I saw a bunch of mini flying people buzzing around a couple of mushrooms!

I don't know why but I've always known I was different. That dream when I was a baby of a woman and a tall blonde man. Or even when the villagers look at me, they all mean something, something that they're hiding.

I woke up to find myself in a white room. I sighed as I heard the familiar beeping noise, the smell of medicine in the air confirmed my thoughts, I was in the hospital… _again!_

I chuckled as I saw my legs and arms were tied up. _'They think this will stop me? Well think again!'_ I grunted as I broke through the binds with ease. I grinned triumphantly as my hands were free again, I flexed them a couple of times before bending over and untied the ropes that held onto my ankles.

I pulled the covers off my body and silently as a mouse. I sneaked out of my room, humming the 'Mission Impossible' theme song.

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"Well I'm out of that hellhole, what now?" I told myself. I currently hiding in the bushes while doctors and nurses were frantically running around like headless chickens. That's when I heard a chuckle from behind me. It was a man with odd bright blue hair and gold catlike eyes. He looked around his mid twenties, he was tall too. But what made him interested was the fact that he could feel his power oozing from him.

_'I can't underestimate this guy or else I'll be done for.'_

"Who are you and what do you want from me?" I said in a calm yet strong voice. He simply grinned and took a step towards me, I shifted myself into a fighting stance showing him I was on guard. He chuckled again and continued to approach me until he was inches away from my face.

"Ne kid~" He said in a singsong voice, "what makes you think I want anything from a shrimp like you?" He said innocently with a shit grinning smile on his stupid face, I growled slightly before taking a deep breath.

"Then why are you here?!"

"Oh~, I'm just here to confirm my thoughts, that's all." He said. I gulped nervously and in a shaky voice I asked him what he trying was trying to confirm.

"From what I heard from my friends, they said you can see 'monsters'." I blushed. Of all the things his friends could have said, it had to be that one.

"It's just my stupid imagination." I said my face still flushed. He stopped grinning and in a cold voice he whispered in my ear.

"Who are you?"

My knees trembled in fear, as I could feel his killer intent. He was to close, I could barely breath. I took a step back and tried to make a run for it but he grabbed my shoulders preventing from escaping.

"N-Naruto U-Uzumaki." I cried and began squirm in his grasp but the man didn't even look like he was struggling to hold me, instead he held he tighter. I whimpered as I could feel his nails digging into my shoulder.

"Well Naruto tell me me, are a spy from Valentine?" He gripped my shoulders tighter drawing out my blood. I cried out in pain but stubbornly refused to let my tears fall.

"S-Stop i-it! It h-hurts!" I used all my strength to push him away. I managed to push him off me.

"I don't know who you are or where you came from but I suggest you leave or I'll call the ninja's on you!"

He looked shocked but then gave a sinister smirk. Before I could even blink he disappeared from my sight. I frantically searched for him, suddenly I felt pain at the back of my head before I passed out.

**TBC**

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**Ayame: Sorry it took a long time, I was busy trying to come up with an idea and when I finally did my mum had to confiscate my computer!**

**Ayame: Well here's the second chappie and on the next chappie we will find out who this mysterious guy is.**

**AYAME DOES NOT OWN NARUTO AND MORTAL INSTRUMENTS... Or do I? *Evil Grin***

**(Just to confirm Naruto/Jonathan doesn't remember his past life only a few glimpsed of it and he's really 10 years old)**

**Oh before I forget: PLEASE REVIEW!**


	3. Warlocks, Faeries, Shadowhunters! WTF!

**Chapter 2: Warlocks, Faeries, Shadowhunters?! WTF?!**

"So does he work for Valentine?" Asked a girl with red hair and shocking golden pupil less eyes to the blue haired man in front of her.

"If he was I would have killed him there and then." He said in a teasing tone. He ran his hand through his hair and walked through the hall with the red head following shortly behind him.

"How do you know though?" She asked opening the door to the blonde kid's room. The man walked in and took off his black coat and hanged it on the hook behind the door. There the two were greeted with a sleeping blonde and a brown haired girl with pretty emerald eyes.

"Hello Eve, how is he?"

The girl named Eve blushed shyly. She told him the boy would wake in a few minutes. He nodded and waved his hand in a dismissing action. Eve hurriedly exited the room, shutting the door as quietly as possible.

"To continue our conversation, I threatened to kill him," He said simply, the red head sweat dropped. "What?! It works! The kid didn't show any signs of lying, he was telling the truth!"

"Typical Marcello." She said shaking her head. The man named Marcello pouted like a child, crossing his arms doing so.

"To tell you the truth, I think the brat is a newly turned. I mean the boy doesn't even know about Valentine… at _all_."

"Yeah, so? What does got to do with anything?"

He sighed shaking his head, he turned and looked at the girl straight in the eye before looking away. He walked towards a silky creme colored sofa and sank on the comfortable seat, he patted the space next to him, indicating to the girl to sit next to him. The girl hesitated but sat down next him anyway.

"Everyone knows about Valentine ever since the Uprising, the only people I can think of who don't are mundanes or newly turned Downworlders, Lucy."

Lucy looked as if she was to speak. But she froze as random blankets were thrown on the floor.

"W-Where am I?" Said a shaky voice belonging to a child. Marcello bent and picked the blankets from the ground and placed them on the spot on where he was sitting before.

"I-It's you!" The blonde pointed at Marcello. He could only stare at Marcello's golden eyes in fear and awe.

"Don't worry, I won't hurt you, Naruto." Marcello said in a gentle and kind voice, as he attempted to calm the child down.

"I-I don't believe you!" The boy cried and whimpered as a pair of arms circled around his body. It was Lucy, rubbing his back and whispering soothing words to the frightened boy.

"Don't worry, Naru-chan! I'll handle the meanie, Marcello!" Lucy got into a superhero pose which caused Naruto to giggle cutely. Marcello took a step forward causing the boy to flinch.

"I know you're confused but we promise we won't hurt you, ok?" Marcello whispered quietly and smiled softly as the boy's shoulder relaxed.

"Ok." He said quietly.

"Ne Naru-chan, have you ever talked to the Night Children before or even vampires and werewolves?" Lucy asked. Naruto looked at her as she was crazy. Seriously vampires?! Who believes in that garbage?

"Lucy, your going to fast on the kid," He whispered to the girl who blushed a bright shade of red.

"What we mean is that you, Lucy and I are different from all the other people you might know."

"Then what are we?" Naruto asked curiously. He bit his lips and fidgeted on the bed anxiously. Marcello plopped on the coach and let out a long sigh.

"Well firstly, I'll start by telling you about demons. You see demons are like insects, not the _good_ type, the _bad_ type. Their nothing more then pests, they travel to different worlds sucking it's life energy until all is gone. Seeing this a Warlock summoned the angel Raziel. He came down to the Shadow World and offered his blood into a cup, which is now known as the Mortal Cup. Anyway, those who drank from the cup turned into Nephilims, but now we call them Shadowhunters."

"What do they do?"

"Well," Marcello scratched his head sheepishly. "I've never met one."

"EH?!" Two voices cried out at the same time. Naruto looked at Lucy in shock.

"How come you don't know? You've known him for a long time haven't you?"

"I've only known Marcello for 3 years now, it's a surprise actually after all Marcello is _more_ then two _centuries_ years old." Lucy chuckled as Marcello pouted. He was very sensitive about his age.

"You know brat, you're actually taking this very well. I kind of expected you to make a big fuss." Marcello said. Naruto grinned happily, as Marcello showered him with praises.

"Alright before the kids head gets any bigger. We still have to find out what he is." Lucy rubbed her temple as she watched Marcello rub his cheek on the blonde boy who was a deep scarlet red.

"Righto! Let's see." The two mused inspecting he boy, as he sat there uncomfortably under their glance.

"A pixie or a faerie maybe?"

"He's got the looks but I get the feeling he's not, but good guess anyway Lucy!"

"Werewolf?"

"NUH!"

**~ Time Skip: 30 mins later ~**

"We've named all the possible choices yet he's not a single one of them!" Lucy groaned banging her head on the arm of the sofa. Marcello was in a deep thought, not listening to her whining.

"I've got a suspicion on what he might be, although I'm only 23% sure." He mused partly to himself.

"Oh? What's that?" Lucy spared a glance at the blonde boy who was sound asleep, snoring ever so slightly. She was curious too on what type of Downworlder the boy might be.

"Shadowhunter." Was Marcello's quick reply. Lucy felt faint. A Shadowhunter?! That's got to be the most silliest idea ever! Yet looking at the boy once more, she couldn't help but agree with Marcello. He was innocent, strong willed and was pure. Lucy looked away. Pretty soon, that pure white will be tainted with cold black as he faces this cruel yet beautiful world.

"But like I said, I'm only 23% sure."

**TBC**

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**Ayame: Sorry, it took so long. :(**

**Ayame: I couldn't do much writing because of school, that or the fact my mum confiscated my computer.**

**Ayame: So now we know a little more about my OC's. Marcello is a ****_little_**** bipolar, isn't he?**

**Ayame: Lastly if you have any questions please write your questions down on your reviews. (Please review ;A;)**

**AYAME DOES NOT OWN NARUTO OR MORTAL INSTRUMENTS!**


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